Publications by authors named "Alexander E Urban"

41Publications

Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons.

Biol Psychiatry 2020 Jul 1. Epub 2020 Jul 1.

Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California; Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.biopsych.2020.06.021DOI Listing
July 2020

Structural variation in the sequencing era.

Nat Rev Genet 2020 03 15;21(3):171-189. Epub 2019 Nov 15.

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1038/s41576-019-0180-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402362PMC
March 2020

Neural signatures of sleep in zebrafish.

Nature 2019 07 10;571(7764):198-204. Epub 2019 Jul 10.

Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1336-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081717PMC
July 2019

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.

Science 2019 04;364(6436)

Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1126/science.aau8650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7580864PMC
April 2019

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools.

Sci Data 2018 12 18;5:180261. Epub 2018 Dec 18.

Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/sdata.2018.261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298255PMC
December 2018

Local and global chromatin interactions are altered by large genomic deletions associated with human brain development.

Nat Commun 2018 12 17;9(1):5356. Epub 2018 Dec 17.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.

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http://dx.doi.org/10.1038/s41467-018-07766-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297223PMC
December 2018

Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis.

J Med Genet 2018 11 30;55(11):735-743. Epub 2018 Jul 30.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.

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http://jmg.bmj.com/lookup/doi/10.1136/jmedgenet-2018-105272
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http://dx.doi.org/10.1136/jmedgenet-2018-105272DOI Listing
November 2018

Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants.

Methods Mol Biol 2018 ;1768:173-190

Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7778-9_11DOI Listing
February 2019

An 80-Year-Old Man With Asbestos Exposure Presenting With Respiratory Distress.

Chest 2017 08;152(2):e25-e28

Department of Pulmonary and Critical Care, University of Tennessee HSC, Memphis, TN. Electronic address:

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http://dx.doi.org/10.1016/j.chest.2017.03.016DOI Listing
August 2017

Pdlim7 Regulates Arf6-Dependent Actin Dynamics and Is Required for Platelet-Mediated Thrombosis in Mice.

PLoS One 2016 28;11(10):e0164042. Epub 2016 Oct 28.

Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164042PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085081PMC
June 2017

A role of genomic copy number variation in the complex behavioral phenotype of alcohol dependence: a commentary.

Alcohol Clin Exp Res 2012 Sep 21;36(9):1483-6. Epub 2012 Aug 21.

Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Palo Alto, California, USA.

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http://dx.doi.org/10.1111/j.1530-0277.2012.01915.xDOI Listing
September 2012

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

PLoS One 2011 30;6(11):e27859. Epub 2011 Nov 30.

Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027859PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227574PMC
April 2012

Identification of genomic indels and structural variations using split reads.

BMC Genomics 2011 Jul 25;12:375. Epub 2011 Jul 25.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1186/1471-2164-12-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161018PMC
July 2011

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Genome Res 2011 Jun 7;21(6):974-84. Epub 2011 Feb 7.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.114876.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106330PMC
June 2011

EBNA1 regulates cellular gene expression by binding cellular promoters.

Proc Natl Acad Sci U S A 2009 Dec 22;106(52):22421-6. Epub 2009 Dec 22.

Department of Genetics, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1073/pnas.0911676106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799695PMC
December 2009

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.

Genome Biol 2008 Jan 3;9(1):R3. Epub 2008 Jan 3.

Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1186/gb-2008-9-1-r3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395237PMC
January 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Global identification of human transcribed sequences with genome tiling arrays.

Science 2004 Dec 11;306(5705):2242-6. Epub 2004 Nov 11.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1103388
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http://dx.doi.org/10.1126/science.1103388DOI Listing
December 2004